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- EMDB-57835: Structure of Importin 7 in complex with RanGTP -

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Basic information

Entry
Database: EMDB / ID: EMD-57835
TitleStructure of Importin 7 in complex with RanGTP
Map data
Sample
  • Complex: Importin 7 in complex with RanGTP
    • Protein or peptide: Importin 7 L homeolog
    • Protein or peptide: GTP-binding nuclear protein Ran
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsImportin 7 / RanGTP / TRANSPORT PROTEIN
Function / homology
Function and homology information


RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / protein localization to nucleolus ...RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / ribosomal protein import into nucleus / GTP metabolic process / nuclear import signal receptor activity / DNA metabolic process / MicroRNA (miRNA) biogenesis / spermatid development / male germ cell nucleus / dynein intermediate chain binding / mitotic sister chromatid segregation / viral process / ribosomal large subunit export from nucleus / nuclear pore / protein export from nucleus / ribosomal subunit export from nucleus / sperm flagellum / ribosomal small subunit export from nucleus / centriole / protein import into nucleus / hippocampus development / mitotic spindle organization / positive regulation of protein import into nucleus / Transcriptional regulation by small RNAs / recycling endosome / small GTPase binding / melanosome / GDP binding / mitotic cell cycle / nuclear envelope / midbody / G protein activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cell division / cadherin binding / protein heterodimerization activity / protein domain specific binding / chromatin binding / GTPase activity / nucleolus / GTP binding / chromatin / protein-containing complex binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Exportin-2, central domain / Cse1 / : / Importin-11-like, TPR repeats / Ran GTPase / Small GTPase Ran-type domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain ...Exportin-2, central domain / Cse1 / : / Importin-11-like, TPR repeats / Ran GTPase / Small GTPase Ran-type domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Importin 7 L homeolog / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFu Z / Chafra F / Freytag B / Huyton T / Gorlich D
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Structure / Year: 2026
Title: Chaperoning by dynamic encasement: Structural basis of linker histone H1 nuclear import
Authors: Fu Z / Chafra F / Freytag B / Huyton T / Gorlich D
History
DepositionApr 29, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57835.png

Downloads & links

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Map

FileDownload / File: emd_57835.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 128 pix.
= 213.504 Å		1.67 Å/pix.
x 128 pix.
= 213.504 Å		1.67 Å/pix.
x 128 pix.
= 213.504 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0022
Minimum - Maximum-0.007780844 - 0.023598341
Average (Standard dev.)0.00007580887 (±0.0007168663)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 213.504 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_57835_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_57835_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_57835_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Importin 7 in complex with RanGTP

EntireName: Importin 7 in complex with RanGTP
Components
  • Complex: Importin 7 in complex with RanGTP
    • Protein or peptide: Importin 7 L homeolog
    • Protein or peptide: GTP-binding nuclear protein Ran
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Importin 7 in complex with RanGTP

SupramoleculeName: Importin 7 in complex with RanGTP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: Importin 7 L homeolog

MacromoleculeName: Importin 7 L homeolog / type: protein_or_peptide / ID: 1 / Details: Importin 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 119.553156 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDPNILIEAL RGTMDPALRE AAERQLNESH KSLHFVSTLL QITMSEQLEL PVRQAGVIYL KNMITQYWPD REVTPGELPP HTIPEEDRH CIRENIVEAI MHSPELIRVQ LTTCIHHIIK HDYPNRWTAV VEKIGFYLQS DNSACWLGIL LCLYQLVKNY E YKKPEERS ...String:
MDPNILIEAL RGTMDPALRE AAERQLNESH KSLHFVSTLL QITMSEQLEL PVRQAGVIYL KNMITQYWPD REVTPGELPP HTIPEEDRH CIRENIVEAI MHSPELIRVQ LTTCIHHIIK HDYPNRWTAV VEKIGFYLQS DNSACWLGIL LCLYQLVKNY E YKKPEERS PLIAAMQHFL PMLKDRYIQL LADPSEQSVL IQKQIFKIFY ALVQYTLPLE LINQQNLAEW IEILKTVVDR DV PAETLQV DEDDRPELPW WKCKKWALHI LARLFERYGS PGNVSKEYND FAEVFLKAFA VGVQQVLLKV LYQYKEKQYI APR VLQQTL NYFNQGVSHA VTWKNLKPHI QGIIQDVIFP LMCYTDSDED LWQEDPYEYI RMKFDVFEDF ISPTTAAQTL LFTS CSKRK EVLQKTMGFC YQILTEPAAD PRKKDGALHM IGSLAEILLK KKIYKDQMEF MLQNHVFPLF SSELGYMRAR ACWVL HYFC EVKFKVDQNL QTALELTRRC LIDDREMPVK VEAAIALQVL ISNQEKAKEY IVPFIRPVMQ ALLHIIRETE NDDLTN VIQ KMICEYSEEV TPIAVEMTQH LAMTFNQVIQ TGPDEEGSDD KAVTAMGILN TIDTLLSVVE DHKEITQQLE GICLQVI GT VLQQHVLEFY EEIFSLAHSL TCQQVSPQMW QLLPLVFDIF QQDGFDYFTD MMPLLHNYVT VDTDTLLSDT KYLEMIYS M CKKILTGVAG EDAECHAAKL LEVVILQCKG RGIDQVIPLF VEAALERLTR EVKTSELRTM CLQVAIAALY YSPPLLFNT LENLRFPNNE EPVTNHFIKQ WLNDVDCFLG LHDRKICVLG LCALIELEQR PQVLNQMSSQ ILPAFLLLFN GLKRAYACHA EQENDSDDD GDGEDDEDAA ELGSDEDDID EEGQEYLEIL AKQAGEDGDD EDWEDDDAEE TALEGYTTLL DDEDTPIDEY Q IFKAIFQK LQGRDPVWYQ ALTQGLNEDQ GKQLQDIATL ADQRRAAHES KMIEKHGGYK FNAPVVPSTF NFGNPAPGMN

UniProtKB: Importin 7 L homeolog

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Macromolecule #2: GTP-binding nuclear protein Ran

MacromoleculeName: GTP-binding nuclear protein Ran / type: protein_or_peptide / ID: 2 / Details: GTP-binding nuclear protein Ran Q69L / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.135434 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EPQVQFKLVL VGDGGTGKTT FVKRHLTGEF EKKYVATLGV EVHPLVFHTN RGPIKFNVWD TAGLEKFGGL RDGYYIQAQC AIIMFDVTS RVTYKNVPNW HRDLVRVCEN IPIVLCGNKV DIKDRKVKAK SIVFHRKKNL QYYDISAKSN YNFEKPFLWL A RKLIGDPN LEFVAMP

UniProtKB: GTP-binding nuclear protein Ran

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Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Sample volume: 2 microliters blotting time: 5 s blot force setting: 6.
DetailsThe complex was further purified by size exclusion chromatography using a Superdex 200 16/600 column. The purified complex was applied to a glow-discharged grid after being diluted to 0.8 mg/ml.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12532 / Average electron dose: 49.2 e/Å2
Details: Counting mode 5 images per hole ( beam-image shift)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 8100
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1097208
CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: The ab-initio 3D model was generated from particles from good 2D classes using RELION (version 5.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.1) / Number images used: 675579
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 5.0.1)
FSC plot (resolution estimation)

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